AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG033346

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033346 MtrunA17_Chr6g0474101 88.128 438 2 1 1 388 1 438 0.0 777
MsaG033346 MtrunA17_Chr8g0348461 52.866 314 144 3 71 380 202 515 5.43e-123 365
MsaG033346 MtrunA17_Chr8g0350811 49.544 329 160 3 54 380 576 900 5.75e-115 355
MsaG033346 MtrunA17_Chr8g0350811 44.878 205 104 4 72 269 240 442 2.11e-49 178
MsaG033346 MtrunA17_Chr2g0331341 28.319 226 133 7 99 295 3 228 2.32e-16 78.2
MsaG033346 MtrunA17_Chr3g0140101 29.302 215 127 9 99 288 193 407 3.15e-13 70.9
MsaG033346 MtrunA17_Chr8g0381281 26.316 228 117 6 79 288 232 426 4.23e-13 70.5
MsaG033346 MtrunA17_Chr1g0154301 24.746 295 189 12 93 376 105 377 5.31e-13 70.1
MsaG033346 MtrunA17_Chr1g0154301 28.205 234 140 8 99 307 218 448 1.57e-12 68.9
MsaG033346 MtrunA17_Chr4g0059031 25.532 282 174 12 96 351 398 669 4.35e-12 67.8
MsaG033346 MtrunA17_Chr4g0034121 28.125 224 129 9 99 292 245 466 8.45e-12 66.6
MsaG033346 MtrunA17_Chr2g0284241 25.514 243 150 10 97 316 90 324 1.19e-11 65.5
MsaG033346 MtrunA17_Chr5g0440471 27.749 191 122 7 157 337 215 399 9.14e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033346 AT4G25440.2 63.033 422 114 3 1 380 3 424 0.0 564
MsaG033346 AT4G25440.3 63.033 422 114 3 1 380 3 424 0.0 564
MsaG033346 AT4G25440.1 63.033 422 114 3 1 380 3 424 0.0 564
MsaG033346 AT5G51980.1 60.920 435 119 4 1 384 1 435 0.0 559
MsaG033346 AT5G51980.2 60.920 435 119 4 1 384 1 435 0.0 559
MsaG033346 AT5G40880.2 50.462 325 157 3 54 376 114 436 1.20e-114 342
MsaG033346 AT5G40880.1 50.462 325 157 3 54 376 143 465 1.77e-114 342
MsaG033346 AT5G49200.1 49.518 311 152 3 70 375 101 411 3.30e-108 324
MsaG033346 AT1G24530.1 27.143 210 131 7 99 288 194 401 4.18e-14 73.9
MsaG033346 AT3G50390.1 22.581 279 176 8 136 376 93 369 1.19e-13 72.8
MsaG033346 AT3G50390.1 27.602 221 131 8 99 293 210 427 5.30e-11 64.3
MsaG033346 AT1G24130.1 26.606 218 132 7 99 288 191 408 2.89e-13 71.2
MsaG033346 AT1G49040.1 26.820 261 172 7 89 341 888 1137 1.74e-11 66.6
MsaG033346 AT1G47610.1 27.103 214 131 6 99 288 134 346 2.08e-11 65.1
MsaG033346 AT4G32990.1 23.739 337 196 15 89 381 9 328 2.88e-11 64.7
MsaG033346 AT2G26060.1 25.145 346 196 17 93 381 13 352 3.01e-11 64.7
MsaG033346 AT3G18140.1 25.941 239 150 11 97 316 75 305 3.90e-11 63.9
MsaG033346 AT2G26490.1 29.464 224 122 10 99 293 205 421 5.86e-11 64.3
MsaG033346 AT4G15900.1 28.431 204 127 9 96 286 172 369 5.88e-11 64.3

Find 99 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTTACCTTAACAAAAT+TGG 0.095005 6:-84112858 None:intergenic
CCCACTTTATTGCACGTTAT+TGG 0.189410 6:-84115273 None:intergenic
GAGCCAGCTGCATCACTTAA+AGG 0.244802 6:+84113467 MsaT033346.1:CDS
TGGTGATGTCTGTTCTTTGC+TGG 0.262948 6:+84113726 MsaT033346.1:CDS
CTTGCAGGATGGAGCTATAT+TGG 0.296931 6:+84113412 MsaT033346.1:intron
AGTGAATTGCCTACTTCTAA+TGG 0.301502 6:+84111271 MsaT033346.1:CDS
TTATTGGATGTGGCCGGTTC+AGG 0.316183 6:-84115257 None:intergenic
GGAGCTAATAGACTTTATTC+TGG 0.326721 6:+84113521 MsaT033346.1:CDS
TTTCTTACCTTAACAAAATT+GGG 0.332855 6:-84112857 None:intergenic
ATTGCAAGAGCATAGAAGTA+TGG 0.349106 6:-84114533 None:intergenic
TGTCTAATGAACAAGATATA+AGG 0.355225 6:-84113757 None:intergenic
CACTCTTGGAATGTTGGTGA+TGG 0.368628 6:+84111532 MsaT033346.1:CDS
TCAGCATAAGCCCGTTTAGA+AGG 0.378915 6:-84111304 None:intergenic
GGTTCGGATAAGCTTTATAC+TGG 0.382445 6:+84112545 MsaT033346.1:CDS
GGTGTAAGTTTCTTCACTCT+TGG 0.386356 6:+84111518 MsaT033346.1:CDS
TAGACTTTATTCTGGTTCAA+TGG 0.390656 6:+84113529 MsaT033346.1:CDS
ATGATGAGACTGTAAGGGTT+TGG 0.396519 6:+84112573 MsaT033346.1:CDS
AGGGTTTGGGACTGCCAGTC+TGG 0.408736 6:+84112587 MsaT033346.1:CDS
TGATGAGACTGTAAGGGTTT+GGG 0.409539 6:+84112574 MsaT033346.1:CDS
TGCTACGGAAAGTGGAAATC+TGG 0.412766 6:+84113874 MsaT033346.1:CDS
GTAAACACTGCAAGGTTTCA+AGG 0.414343 6:-84113679 None:intergenic
ATTAATGATATGCTCTTTGC+TGG 0.418363 6:+84113079 MsaT033346.1:CDS
ATTCAAGGGAATTGTAGTTA+TGG 0.419571 6:+84111490 MsaT033346.1:intron
GCCAAGTGAGAGTGTGGAAT+TGG 0.422825 6:+84115231 MsaT033346.1:CDS
TCTTTGTTGACTCAGCTTGA+AGG 0.427109 6:+84111559 MsaT033346.1:CDS
GGAATTGTAGTTATGGAGAT+AGG 0.434741 6:+84111497 MsaT033346.1:CDS
GGTGATGTCTGTTCTTTGCT+GGG 0.435801 6:+84113727 MsaT033346.1:CDS
GAAGTAATGATGAGACTGTA+AGG 0.438934 6:+84112567 MsaT033346.1:CDS
TTTCTTCACTCTTGGAATGT+TGG 0.440764 6:+84111526 MsaT033346.1:CDS
TTGGGACTGCCAGTCTGGAC+AGG 0.443226 6:+84112592 MsaT033346.1:CDS
GTGAATTGCCTACTTCTAAT+GGG 0.444534 6:+84111272 MsaT033346.1:CDS
AGGTAAGATATTCAACAAAC+AGG 0.445583 6:+84115151 MsaT033346.1:CDS
AATTGCTATGCCCTCTGGTT+CGG 0.446239 6:+84112529 MsaT033346.1:CDS
TAGGGTATAATCACCCTTTG+TGG 0.446419 6:+84114487 MsaT033346.1:intron
GGAATGGTGCTCCTTCTAAA+CGG 0.446924 6:+84111293 MsaT033346.1:CDS
TTCTTCACTGGTGATGGAAC+TGG 0.448650 6:+84115209 MsaT033346.1:CDS
GGCAATTCACTATGCAGAAA+AGG 0.455554 6:-84111259 None:intergenic
TTCATTAGACAAAACAGTAA+AGG 0.464680 6:+84113769 MsaT033346.1:CDS
CGTGTTTACAATCGTCTTGG+TGG 0.467498 6:+84111160 MsaT033346.1:CDS
TCAATGGAGATAAGTCTAGA+TGG 0.468495 6:+84113025 MsaT033346.1:CDS
TTGAATGAACAGGTTGTAAG+TGG 0.476227 6:+84112506 MsaT033346.1:intron
GAATGGTGCTCCTTCTAAAC+GGG 0.477698 6:+84111294 MsaT033346.1:CDS
TGTATAGCTGTGATCAATCT+TGG 0.477996 6:+84112782 MsaT033346.1:CDS
TTATTGCACGTTATTGGATG+TGG 0.479439 6:-84115267 None:intergenic
ACTCTTGGAATGTTGGTGAT+GGG 0.480654 6:+84111533 MsaT033346.1:CDS
AGTGGAATTGCTATGCCCTC+TGG 0.484501 6:+84112524 MsaT033346.1:CDS
AGCATATTCTTCACTGGTGA+TGG 0.496351 6:+84115203 MsaT033346.1:CDS
GGTGTTGTTTCGTTAGTTGT+TGG 0.496526 6:+84113500 MsaT033346.1:CDS
CGAGCAATTCAGACTGGTCC+TGG 0.502735 6:+84115179 MsaT033346.1:CDS
CCTGGTAGCATATTCTTCAC+TGG 0.512028 6:+84115197 MsaT033346.1:CDS
GTGTGGTATGCTACGGAAAG+TGG 0.514044 6:+84113866 MsaT033346.1:CDS
TGCATCATGCATCCCACAAA+GGG 0.514045 6:-84114500 None:intergenic
AGGGTATAATCACCCTTTGT+GGG 0.517484 6:+84114488 MsaT033346.1:intron
TCCAATTCCACACTCTCACT+TGG 0.520959 6:-84115232 None:intergenic
GTATGATCAGTGAAGGTCCC+TGG 0.528209 6:+84112819 MsaT033346.1:CDS
AAGCGTGTTTACAATCGTCT+TGG 0.534374 6:+84111157 MsaT033346.1:CDS
TTTGTTTCTATGGATTTCGA+CGG 0.545744 6:+84111127 None:intergenic
GTGGAATTGGATACCTGAAC+CGG 0.547100 6:+84115244 MsaT033346.1:CDS
TGCACGTTATTGGATGTGGC+CGG 0.547273 6:-84115263 None:intergenic
ATTCTTTGAATCACCACCGT+TGG 0.549048 6:-84111185 None:intergenic
TCAGCTTGAAGGACATAAGA+AGG 0.550026 6:+84111570 MsaT033346.1:CDS
TTGTAACAACCTGTCCAGAC+TGG 0.550382 6:-84112601 None:intergenic
TTGCAAGAGCATAGAAGTAT+GGG 0.552250 6:-84114532 None:intergenic
AATCGTCTTGGTGGGTCCAA+CGG 0.554468 6:+84111169 MsaT033346.1:CDS
TTGGAACACACAAAATTCAA+TGG 0.554692 6:+84113009 MsaT033346.1:CDS
TATGCTCTTTGCTGGTACGC+AGG 0.562187 6:+84113087 MsaT033346.1:CDS
GCACCATTCCCATTAGAAGT+AGG 0.568465 6:-84111280 None:intergenic
GTGTTTACAATCGTCTTGGT+GGG 0.570120 6:+84111161 MsaT033346.1:CDS
TTGTTCAGATTTGCAGAGAG+AGG 0.570280 6:+84115131 MsaT033346.1:intron
GTTTCTATGGATTTCGACGG+TGG 0.572025 6:+84111130 None:intergenic
AACTAACGAAACAACACCAC+GGG 0.575189 6:-84113495 None:intergenic
ATCAATCTTGGCGGTGAAGT+AGG 0.580144 6:+84112794 MsaT033346.1:CDS
AGTGCATAAACTTGTCCCAC+AGG 0.580756 6:-84113049 None:intergenic
TATGCAGGTGTGGTATGCTA+CGG 0.582090 6:+84113859 MsaT033346.1:intron
ATAAAGCTTATCCGAACCAG+AGG 0.585965 6:-84112540 None:intergenic
TTGCCTACTTCTAATGGGAA+TGG 0.590538 6:+84111277 MsaT033346.1:CDS
CAGTGTCTGTAAACACTGCA+AGG 0.596655 6:-84113687 None:intergenic
TGCAGCTGGCTCGAAACAGT+TGG 0.597581 6:-84113456 None:intergenic
TGACCTTTAAGTGATGCAGC+TGG 0.606030 6:-84113470 None:intergenic
ATAAGTCTAGATGGCCCTGT+GGG 0.615106 6:+84113034 MsaT033346.1:CDS
CTTACGACGGCAGATCATAG+AGG 0.618066 6:-84114570 None:intergenic
CCAGTGAAGAATATGCTACC+AGG 0.618179 6:-84115197 None:intergenic
AGGATGGAGCTATATTGGTA+TGG 0.618970 6:+84113417 MsaT033346.1:intron
TCACTATGCAGAAAAGGACA+TGG 0.619738 6:-84111253 None:intergenic
CGTCTTGGTGGGTCCAACGG+TGG 0.620014 6:+84111172 MsaT033346.1:CDS
GTGCATCATGCATCCCACAA+AGG 0.625754 6:-84114501 None:intergenic
GTAGGTTGTATGATCAGTGA+AGG 0.632803 6:+84112812 MsaT033346.1:CDS
ACTGACAGAGCACACGTCTG+TGG 0.634364 6:+84113706 MsaT033346.1:CDS
AAGTAATGATGAGACTGTAA+GGG 0.635516 6:+84112568 MsaT033346.1:CDS
GAGGTGCGAGCAATTCAGAC+TGG 0.636091 6:+84115173 MsaT033346.1:CDS
GAACTGGCCAAGTGAGAGTG+TGG 0.646364 6:+84115225 MsaT033346.1:CDS
ATAGCTGTGATCAATCTTGG+CGG 0.647484 6:+84112785 MsaT033346.1:CDS
GTGCATAAACTTGTCCCACA+GGG 0.654394 6:-84113048 None:intergenic
TAAGATATTCAACAAACAGG+AGG 0.665359 6:+84115154 MsaT033346.1:CDS
TCACTTAAAGGTCATACCCG+TGG 0.682929 6:+84113479 MsaT033346.1:CDS
TGTGGGATGCATGATGCACA+AGG 0.684145 6:+84114505 MsaT033346.1:CDS
TAAAGCTTATCCGAACCAGA+GGG 0.687572 6:-84112539 None:intergenic
CAACTAACGAAACAACACCA+CGG 0.703335 6:-84113496 None:intergenic
GATAAGTCTAGATGGCCCTG+TGG 0.703722 6:+84113033 MsaT033346.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 84111136 84115289 84111136 ID=MsaG033346
Chr6 mRNA 84111136 84115289 84111136 ID=MsaT033346.1;Parent=MsaG033346
Chr6 exon 84111136 84111343 84111136 ID=MsaT033346.1.exon1;Parent=MsaT033346.1
Chr6 CDS 84111136 84111343 84111136 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84111497 84111591 84111497 ID=MsaT033346.1.exon2;Parent=MsaT033346.1
Chr6 CDS 84111497 84111591 84111497 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84112518 84112613 84112518 ID=MsaT033346.1.exon3;Parent=MsaT033346.1
Chr6 CDS 84112518 84112613 84112518 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84112782 84112871 84112782 ID=MsaT033346.1.exon4;Parent=MsaT033346.1
Chr6 CDS 84112782 84112871 84112782 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84113007 84113108 84113007 ID=MsaT033346.1.exon5;Parent=MsaT033346.1
Chr6 CDS 84113007 84113108 84113007 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84113419 84113565 84113419 ID=MsaT033346.1.exon6;Parent=MsaT033346.1
Chr6 CDS 84113419 84113565 84113419 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84113671 84113790 84113671 ID=MsaT033346.1.exon7;Parent=MsaT033346.1
Chr6 CDS 84113671 84113790 84113671 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84113866 84113925 84113866 ID=MsaT033346.1.exon8;Parent=MsaT033346.1
Chr6 CDS 84113866 84113925 84113866 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84114490 84114587 84114490 ID=MsaT033346.1.exon9;Parent=MsaT033346.1
Chr6 CDS 84114490 84114587 84114490 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Chr6 exon 84115139 84115289 84115139 ID=MsaT033346.1.exon10;Parent=MsaT033346.1
Chr6 CDS 84115139 84115289 84115139 ID=cds.MsaT033346.1;Parent=MsaT033346.1
Gene Sequence

>MsaT033346.1

ATGGATTTCGACGGTGGTAATAAGCGTGTTTACAATCGTCTTGGTGGGTCCAACGGTGGTGATTCAAAGAATCAGAAAGTGTGTTTTCAATGGCAAGCAGGAAAGTGTAATCGTTATCCATGTCCTTTTCTGCATAGTGAATTGCCTACTTCTAATGGGAATGGTGCTCCTTCTAAACGGGCTTATGCTGATAATTCGAGTTTTTCTGGGAATTGTAGTTATGGAGATAGGTGTAAGTTTCTTCACTCTTGGAATGTTGGTGATGGGTTTTCTTTGTTGACTCAGCTTGAAGGACATAAGAAGGTTGTAAGTGGAATTGCTATGCCCTCTGGTTCGGATAAGCTTTATACTGGAAGTAATGATGAGACTGTAAGGGTTTGGGACTGCCAGTCTGGACAGTGTATAGCTGTGATCAATCTTGGCGGTGAAGTAGGTTGTATGATCAGTGAAGGTCCCTGGCTTTTTGTGGGCATACCCAATTTTGTTAAGGCTTGGAACACACAAAATTCAATGGAGATAAGTCTAGATGGCCCTGTGGGACAAGTTTATGCACTTGTTGTGATTAATGATATGCTCTTTGCTGGTACGCAGGATGGAGCTATATTGGTATGGAAATTTAATGTAGCTGCCAACTGTTTCGAGCCAGCTGCATCACTTAAAGGTCATACCCGTGGTGTTGTTTCGTTAGTTGTTGGAGCTAATAGACTTTATTCTGGTTCAATGGACAACACAGTCAGAGTGTGGAACCTTGAAACCTTGCAGTGTTTACAGACACTGACAGAGCACACGTCTGTGGTGATGTCTGTTCTTTGCTGGGATCAGTTCCTTATATCTTGTTCATTAGACAAAACAGTAAAGGTGTGGTATGCTACGGAAAGTGGAAATCTGGAAGTGACATATACTCACACTGAAGAACATGGTATAATCACCCTTTGTGGGATGCATGATGCACAAGGCAAGCCCATACTTCTATGCTCTTGCAATGATAACACTGTTCGCCTCTATGATCTGCCGTCATTTGCAGAGAGAGGTAAGATATTCAACAAACAGGAGGTGCGAGCAATTCAGACTGGTCCTGGTAGCATATTCTTCACTGGTGATGGAACTGGCCAAGTGAGAGTGTGGAATTGGATACCTGAACCGGCCACATCCAATAACGTGCAATAA
Protein sequence

>MsaT033346.1

MDFDGGNKRVYNRLGGSNGGDSKNQKVCFQWQAGKCNRYPCPFLHSELPTSNGNGAPSKRAYADNSSFSGNCSYGDRCKFLHSWNVGDGFSLLTQLEGHKKVVSGIAMPSGSDKLYTGSNDETVRVWDCQSGQCIAVINLGGEVGCMISEGPWLFVGIPNFVKAWNTQNSMEISLDGPVGQVYALVVINDMLFAGTQDGAILVWKFNVAANCFEPAASLKGHTRGVVSLVVGANRLYSGSMDNTVRVWNLETLQCLQTLTEHTSVVMSVLCWDQFLISCSLDKTVKVWYATESGNLEVTYTHTEEHGIITLCGMHDAQGKPILLCSCNDNTVRLYDLPSFAERGKIFNKQEVRAIQTGPGSIFFTGDGTGQVRVWNWIPEPATSNNVQ*